☰ Navigation Tabs
Crystal structure of NDM-1 at pH7.5 (Succinate) with 1 molecule per asymmetric unit
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 3Q6X
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 295 0.1M sodium succinate pH7.5, 30% PEG 3350
Crystal Properties Matthews coefficient Solvent content 2.01 38.89
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 41.451 α = 90 b = 59.885 β = 97.94 c = 41.972 γ = 90
Symmetry Space Group P 1 21 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 CCD ADSC QUANTUM 315r 2013-01-03 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON SSRF BEAMLINE BL17U1 0.93924 SSRF BL17U1
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 0.95 50 98.6 0.076 13.6 4.8 125535
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 0.95 0.98 86.3 0.485 3.7
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (Observed) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT 3q6x 0.95 33.88 119202 6297 98.39 0.1132 0.1126 0.1143 0.1246 0.127 RANDOM 10.46
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.04 -0.01 -0.23 0.26
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.134 r_sphericity_free 30.705 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 12.577 r_sphericity_bonded 7.348 r_dihedral_angle_1_deg 6.475 r_angle_refined_deg 1.458 r_angle_other_deg 1.404 r_rigid_bond_restr 1.375 r_chiral_restr 0.081
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 32.134 r_sphericity_free 30.705 r_dihedral_angle_4_deg 17.787 r_dihedral_angle_3_deg 12.577 r_sphericity_bonded 7.348 r_dihedral_angle_1_deg 6.475 r_angle_refined_deg 1.458 r_angle_other_deg 1.404 r_rigid_bond_restr 1.375 r_chiral_restr 0.081 r_bond_refined_d 0.009 r_gen_planes_refined 0.007 r_gen_planes_other 0.003 r_bond_other_d 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 1701 Nucleic Acid Atoms Solvent Atoms 301 Heterogen Atoms 27
Software Software Software Name Purpose DENZO data reduction SCALEPACK data scaling REFMAC refinement PDB_EXTRACT data extraction PHASER phasing